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| Status |
Public on Oct 16, 2019 |
| Title |
Transcriptomics profiling of some commonly used cell lines at the base-line culture condition |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In vivo, melanoma cells transition though distinct phenotypic states in response to a changing microenvironment, and most notably can switch between invasive and proliferative phenotypes characterized by high and low levels of MITF activity (Hoek and Goding, 2010; Hoek et al., 2008). Since melanoma cell lines isolated from human tumors tend also to fall into either proliferative or invasive, slow-growing phenotypes (Hoek et al., 2006), it seems likely that established lines reflect specific phenotypic states within tumors, including those detected using single cell RNA-seq, that are then fixed and maintained under nutrient–rich culture conditions where the microenvironmental stresses encountered in vivo are absent. Indeed, it has been shown that melanoma cell lines presenting distinct phenotypic states exhibit very different responses to microenvironmental cues such as hypoxia (Louphrasitthiphol et al., 2019). The aim of this study is to characterise some of the commonly use cell lines and assign each with a phenotypic state base on its transcriptomics.
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| Overall design |
Indicated cell line were grown in RPMI without any treatment prior to RNA extraction and sequencing
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| |
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| Contributor(s) |
Louphrasitthiphol P, Goding CR |
| Citation(s) |
31733993 |
| |
| Submission date |
Sep 13, 2019 |
| Last update date |
Nov 28, 2019 |
| Contact name |
Pakavarin Louphrasitthiphol |
| E-mail(s) |
pakavarin.louphrasitthiphol@ludwig.ox.ac.uk
|
| Phone |
01865 617543
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Department |
Nuffield Department of Clinical Medicine
|
| Lab |
Prof. CRGoding
|
| Street address |
Old Road Campus Research Building (off Roosevelt Drive)
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| City |
Oxford |
| ZIP/Postal code |
OX3 7DQ |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE137392 |
MITF regulates SCD and fatty acid saturation to control melanoma phenotypic state. |
|
| Relations |
| BioProject |
PRJNA565366 |
| SRA |
SRP221555 |
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